WP2 - Define and Synthesize

About This Grant

RESEARCH ABSTRACT Cancer Grand Challenges Connecting DNA Adducts, Unexplained Mutational Signatures, and Cancer Etiologies (CAUSE) Host Institution: University of California, San Diego Background: Genome sequencing of thousands of cancers has identified over 100 distinct mutational signatures—recurring patterns of somatic mutations that reflect mutagenic processes. While some have known causes, most—including key cancer-driving signatures—remain unexplained. These include endogenous ubiquitous age-associated signatures (e.g., SBS5), tissue-specific processes (e.g., SBS40), and geography-associated patterns likely linked to unknown environmental exposures (e.g., SBS12, SBS89). Biochemically, most somatic mutations arise from misrepair or replication across damaged DNA (i.e., DNA adducts). Cells experience tens of thousands of DNA adducts daily—from both endogenous metabolism and environmental exposures. While most are accurately repaired, some persist leading to permanent changes in the DNA sequence (i.e., somatic mutations). As a result, cancer genomes preserve a durable, but mechanistically obscured, record of genotoxic damage. Understanding the origins of unexplained mutational signatures requires identifying the initiating DNA adducts and dissecting how their formation, persistence, and processing shape mutational patterns. Aims: The Connecting Adducts, Unexplained Signatures, and Cancer Etiologies (CAUSE) project aims to mechanistically understand unexplained mutational signatures by systematically identifying specific DNA adducts and linking them to the mutations they generate. CAUSE will build a high-throughput discovery platform that integrates chemistry, biology, genomics and cutting-edge technologies. The project will focus on three mutagenic contexts: (1) endogenous processes underlying signatures like SBS5 and SBS40, (2) likely environmental exposures driving tissue- and geography-specific patterns like SBS12 and SBS89, and (3) chemotherapy-induced DNA adducts, which will be used as a controlled benchmark. The proposed approaches are broadly applicable and will help uncover the origins of many unexplained mutational signatures while advancing next-generation mutagenesis technologies such as a reimagined Ames test. Methods: CAUSE will integrate human tissue analysis with diverse experimental systems—including in vitro assays, cell lines, and mouse models—across seven coordinated modules: (1) mass spectrometry to detect diverse DNA adducts; (2) structural characterization via chemical synthesis and microcrystal electron diffraction; (3) genome-wide lesion mapping using Endo-seq, long-read sequencing, and polymerase-stalling enrichment; (4) single-molecule reporter assays of misrepair in defined repair contexts; (5) biochemical perturbations in Xenopus cell-free systems to dissect repair mechanisms; (6) genetic perturbations in animal models to dissect damage and repair pathways; and (7) interpretable AI to model how lesion features and repair status predict mutational outcomes. Impact: CAUSE will generate the first mechanistic atlas linking DNA adducts to mutational signatures. This foundational resource will enable causal attribution, clarify age- and exposure-related mutagenesis, and shift mutational signature research from observational to actionable—transforming cancer prevention, diagnosis, and care.